Orofacial clefts are one of the most commonly occurring human birth defects, yet the underlying causes remain largely unknown. Genome wide association studies indicate heritability for such defects, however the vast majority of associations fall outside of genes suggesting defective gene regulation is a major contributor. The proposed work seeks to identify the genetic causes of nonsyndromic cleft lip and palate (NSCLP) by identifying and characterizing gene regulatory sequences that are active in early human orofacial development and disrupted in affected individuals. Preliminary research using functional genomics methods directly in human embryonic tissue has identified thousands of potential orofacial regulatory sequences, including several that are in linkage disequilibrium with single nucleotide polymorphisms strongly associated with NSCLP. This Pathway to Independence award application includes a mentored career development plan for transition of the candidate, Dr. Justin Cotney, into an independent investigator, as well an accompanying research plan describing the proposed experiments on identification and characterization of disease-associated variants in gene regulatory sequences. The candidate, Dr. Cotney, is a postdoctoral fellow at Yale University School of Medicine, in the lab of Dr. James Noonan in the Department of Genetics. The work leading to his graduate degree in Genetics and Molecular Biology at Emory University was conducted in the lab of Dr. Gerald Shadel in the Department of Biochemistry at Emory and Department of Genetics at Yale. There he focused on understanding the contributions of two members of a novel class of transcription factors to human mitochondrial gene expression and retrograde signaling. In the Noonan lab, Dr. Cotney applied biochemical and computational methods to identify gene regulatory sequences directly in embryonic limb tissue that have contributed to human-specific evolution of the hand and foot. The techniques and computational methods to address these evolutionary questions in embryonic development can be adapted to understand gene regulation in any developing tissue, placing Dr. Cotney in a unique position to investigate the causes of NSCLP. The mentoring and career development plan detailed within will supplement his background in basic molecular biology and functional genomics with additional training and instruction in statistical genetics and human orofacial development. Dr. Cotney's goal is to become a faculty member in an interdisciplinary bioscience, developmental biology, or similar department at an academic institution, in which he can research the role of dysfunction of developmental gene regulation in common human diseases. The research plan will leverage Dr. Cotney's expertise in functionally profiling embryonic tissue to identify gene regulatory sequences that are active during the formation of pharyngeal arches to fusion of palates and facial structures. The project further proposes to determine which of these activated regulatory elements are burdened with variants and structural changes in NSCLP patients and identify the consequences of disrupted developmental gene regulation. The identification of gene regulatory networks that are commonly perturbed in NSCLP patients will provide genetic markers that can predict the occurrence of these defects and provide targets for future preventative or therapeutic measures. Alleviating the impact of orofacial clefts and preventing their occurrence will increase global public health and lift a large financial burden currently faced by affected individuals and their families.